mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-10-02 06:20:49 +02:00
Cleaning, Pep 8
This commit is contained in:
Thomas Applencourt
parent
5c2e20af96
commit
18bc6bf347
@ -11,9 +11,9 @@ Usage:
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EMSL_api.py list_atoms --basis=<basis_name>
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[--db_path=<db_path>]
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EMSL_api.py get_basis_data --basis=<basis_name>
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[--atom=<atom_name>...]
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[--db_path=<db_path>]
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[(--save [--path=<path>])]
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[--atom=<atom_name>...]
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[--db_path=<db_path>]
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[(--save [--path=<path>])]
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EMSL_api.py list_formats
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EMSL_api.py create_db --db_path=<db_path>
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--format=<format>
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@ -59,47 +59,100 @@ def checkSQLite3(db_path):
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def cond_sql_or(table_name, l_value, glob=False):
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"""Take a table_name, a list of value and create the sql or combande"""
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opr = "GLOB" if glob else "="
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l = []
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dmy = " OR ".join(['%s %s "%s"' % (table_name, opr, i) for i in l_value])
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if dmy:
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l.append("(%s)" % dmy)
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return l
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return [" OR ".join(['{} {} "{}"'.format(table_name,
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opr,
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val) for val in l_value])]
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def string_to_nb_mo(str_l):
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def string_to_nb_mo(str_type):
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"""Take a string and return the nb of orbital"""
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assert len(str_type) == 1
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assert len(str_l) == 1
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d = {"S": 1,
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"P": 2,
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"D": 3}
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d = {"S": 3,
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"P": 5,
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"D": 7}
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if str_l in d:
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return d[str_l]
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if str_type in d:
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return 2 * d[str_type] + 1
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# ord("F") = 70 and ord("Z") = 87
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elif 70 <= ord(str_l) <= 87:
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elif 70 <= ord(str_type) <= 87:
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# ord("F") = 70 and l = 4 so ofset if 66
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return 2 * (ord(str_l) - 66) + 1
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return 2 * (ord(str_type) - 66) + 1
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else:
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raise BaseException
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# _
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# / |_ _ _ | _. | o _| o _|_
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# \_ | | (/_ (_ |< \/ (_| | | (_| | |_ \/
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# /
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def check_gamess(str_type):
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"""Check is the orbital type is handle by gamess"""
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assert len(str_type) == 1
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if str_type in "S P D".split():
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return True
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elif str_type > "L":
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raise BaseException
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else:
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return True
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def check_NWChem(str_type):
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"""Check is the orbital type is handle by gamess"""
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assert len(str_type) == 1
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if str_type in "S P D".split():
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return True
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elif str_type > "I" or str_type in "K L M".split():
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raise BaseException
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else:
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return True
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# _ __
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# |_ |\/| (_ | | _ _ _. |
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# |_ | | __) |_ |_ (_) (_ (_| |
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#
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class EMSL_local:
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"""
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All the method for using the EMSL db localy
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"""
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import re
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def __init__(self, db_path=None):
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self.db_path = db_path
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self.p = re.compile(ur'^(\w)\s+\d+\b')
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def get_list_type(self, atom_basis):
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"""
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Return the begin and the end of all the type of orbital
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input: atom_basis = [name, ]
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output: [ [type, begin, end], ...]
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"""
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# Example
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# [[u'S', 1, 5], [u'L', 5, 9], [u'L', 9, 12], [u'D', 16, 18]]"
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l = []
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for i, line in enumerate(atom_basis):
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m = re.search(self.p, line)
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if m:
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l.append([m.group(1), i])
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try:
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l[-2].append(i)
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except IndexError:
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pass
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l[-1].append(i + 1)
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return l
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def get_list_basis_available(self,
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elts=[],
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basis=[],
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@ -122,17 +175,17 @@ class EMSL_local:
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# G e t i n g B a s i s _ i d #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# ~#~#~#~#~#~ #
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# F i l t e r #
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# ~#~#~#~#~#~ #
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if basis:
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cmd_basis = " ".join(cond_sql_or("name", basis, glob=True))
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else:
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cmd_basis = "(1)"
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# Not Ets
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if not elts:
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if not average_mo_number:
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cmd = """SELECT DISTINCT name, description
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FROM basis_tab
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@ -145,6 +198,11 @@ class EMSL_local:
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cmd = cmd.format(cmd_basis)
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else:
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# G e t t i n g _ B a s i s I d #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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str_ = """SELECT DISTINCT basis_id
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FROM output_tab
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WHERE elt=? AND {0}""".format(cmd_basis)
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@ -156,19 +214,24 @@ class EMSL_local:
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cmd_basis = " ".join(cond_sql_or("basis_id", dump))
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cmd_ele = " ".join(cond_sql_or("elt", elts))
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# C r e a t e _ t h e _ c m d #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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column_to_fech = "name, description"
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if average_mo_number:
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column_to_fech += ", data"
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filter_where = cmd_ele + " AND " + cmd_basis
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cmd = """SELECT DISTINCT {0}
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FROM output_tab
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WHERE {1}
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ORDER BY name"""
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ORDER BY name""".format(column_to_fech, filter_where)
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if average_mo_number:
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column = "name, description, data"
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else:
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column = "name, description"
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filter_ = cmd_ele + " AND " + cmd_basis
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cmd = cmd.format(column, filter_)
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# ~#~#~#~#~ #
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# F e t c h #
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# ~#~#~#~#~ #
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c.execute(cmd)
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info = c.fetchall()
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@ -184,14 +247,11 @@ class EMSL_local:
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# Description : dict_info[name] = [description, nb_mo, nb_ele]
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if average_mo_number:
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for name, description, data in info:
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for name, description, atom_basis in info:
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nb_mo = 0
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for line in data.split("\n")[1:]:
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str_l = line.split()[0]
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try:
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nb_mo += string_to_nb_mo(str_l)
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except BaseException:
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pass
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for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
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nb_mo += string_to_nb_mo(type_)
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try:
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dict_info[name][1] += nb_mo
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@ -210,31 +270,50 @@ class EMSL_local:
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def get_list_element_available(self, basis_name):
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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str_ = "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE"
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# ~#~#~#~#~#~ #
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# F i l t e r #
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# ~#~#~#~#~#~ #
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str_ = """SELECT DISTINCT elt
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FROM output_tab
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WHERE name=:name_us COLLATE NOCASE"""
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# ~#~#~#~#~ #
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# F e t c h #
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# ~#~#~#~#~ #
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c.execute(str_, {"name_us": basis_name})
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data = c.fetchall()
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data = [str(i[0]) for i in data]
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conn.close()
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return data
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def get_basis(self, basis_name, elts=None):
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# ~#~#~#~#~#~ #
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# R e t u r n #
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# ~#~#~#~#~#~ #
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return [str(i[0]) for i in c.fetchall()]
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def get_basis(self, basis_name, elts=None, checking=None):
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"""
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Return the data from the basis set
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"""
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# __ _
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# /__ _ _|_ _|_ ._ _ ._ _ _ _. |
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# \_| (/_ |_ | | (_) | | | _> (_| |
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# |
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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# ~#~#~#~#~#~ #
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# F i l t e r #
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# ~#~#~#~#~#~ #
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cmd_ele = " ".join(cond_sql_or("elt", elts)) if elts else "(1)"
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c.execute('''SELECT DISTINCT data from output_tab
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@ -243,10 +322,25 @@ class EMSL_local:
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cmd_ele=cmd_ele))
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# We need to take i[0] because fetchall return a tuple [(value),...]
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l_data_raw = [i[0].strip() for i in c.fetchall()]
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l_atom_basis = [i[0].strip() for i in c.fetchall()]
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conn.close()
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return l_data_raw
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# ~#~#~#~#~ #
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# C h e c k #
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# ~#~#~#~#~ #
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checking = False
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if checking:
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for atom_basis in l_atom_basis:
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for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
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check_gamess(type_)
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# ~#~#~#~#~#~ #
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# R e t u r n #
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# ~#~#~#~#~#~ #
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return l_atom_basis
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if __name__ == "__main__":
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